def test_invalid_eamp_character(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
epidb.add_biosource(
"rostrolateral thalamic nucleus of Butler <methodName>Saidel", "",
{}, self.admin_key)
epidb.add_biosource("testing <b>cool", "", {}, self.admin_key)
epidb.add_biosource("testing ugly &Saidel", "", {}, self.admin_key)
epidb.add_biosource("testing weird <Saidel", "", {}, self.admin_key)
epidb.add_biosource("testing open Saidel>", "", {}, self.admin_key)
epidb.add_biosource("testing closed <Saidel>", "", {}, self.admin_key)
epidb.add_biosource("!'234456789<<<<><<<;;.,.,-,>", "", {},
self.admin_key)
(r, a) = epidb.list_biosources(None, self.admin_key)
self.assertSuccess(r, a)
biosource_names = [x[1] for x in a]
self.assertEquals(biosource_names, [
'K562', 'Brain',
'rostrolateral thalamic nucleus of Butler <methodName>Saidel',
'testing <b>cool', 'testing ugly &Saidel', 'testing weird <Saidel',
'testing open Saidel>', 'testing closed <Saidel>',
"!'234456789<<<<><<<;;.,.,-,>"
])
def test_biosource_scope(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init(epidb)
self.assertSuccess(epidb.add_biosource("GM12878", None, {}, self.admin_key))
self.assertSuccess(epidb.add_biosource("K562", None, {}, self.admin_key))
self.assertSuccess(epidb.add_biosource("Adult_CD4_naive", None, {}, self.admin_key))
self.assertSuccess(epidb.add_biosource("blood", None, {}, self.admin_key))
self.assertSuccess(epidb.add_biosource("mesoderm", None, {}, self.admin_key))
res, biosources = epidb.list_biosources(None, self.admin_key)
self.assertSuccess(res, biosources)
biosources_names = epidb.extract_names(biosources)[1]
self.assertEqual(len(biosources), 5)
self.assertTrue("GM12878" in biosources_names)
self.assertTrue("K562" in biosources_names)
self.assertTrue("Adult_CD4_naive" in biosources_names)
self.assertTrue("blood" in biosources_names)
self.assertTrue("mesoderm" in biosources_names)
self.assertSuccess(epidb.set_biosource_parent("blood", "GM12878", self.admin_key))
self.assertSuccess(epidb.set_biosource_parent("blood", "K562", self.admin_key))
self.assertSuccess(epidb.set_biosource_parent("blood", "Adult_CD4_naive", self.admin_key))
self.assertSuccess(epidb.set_biosource_parent("mesoderm", "blood", self.admin_key))
res = epidb.set_biosource_parent("GM12878", "mesoderm", self.admin_key)
self.assertFailure(res)
epidb.set_biosource_parent("avacado", "mesoderm", self.admin_key)
self.assertFailure(res)
res, scope = epidb.get_biosource_children("mesoderm", self.admin_key)
self.assertSuccess(res, scope)
scope_names = epidb.extract_names(scope)[1]
self.assertEquals(scope_names, ['mesoderm', 'blood', 'GM12878', 'K562', 'Adult_CD4_naive'])
self.assertSuccess(epidb.add_biosource("god master", None, {}, self.admin_key))
print epidb.set_biosource_parent("god master", "mesoderm", self.admin_key)
self.assertSuccess(epidb.add_biosource("shitty", None, {}, self.admin_key))
print epidb.set_biosource_parent("K562", "shitty", self.admin_key)
self.assertSuccess(epidb.add_biosource("weirdo", None, {}, self.admin_key))
print epidb.set_biosource_parent("weirdo", "K562", self.admin_key)
def test_remove_biosource(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
res, biosources = epidb.list_biosources(None, self.admin_key)
for biosource in biosources:
res = epidb.remove(biosource[0], self.admin_key)
self.assertFailure(res)
for biosource in biosources:
res, samples = epidb.list_samples(biosource[1], {}, self.admin_key)
for sample in samples:
res = epidb.remove(sample[0], self.admin_key)
self.assertSuccess(res)
for biosource in biosources:
res = epidb.remove(biosource[0], self.admin_key)
self.assertSuccess(res)
def test_biosource(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init(epidb)
self.assertSuccess(epidb.add_biosource("K562", "leukemia cell", {}, self.admin_key))
self.assertSuccess(epidb.add_biosource("K562b", "leukemia cell", {}, self.admin_key))
self.assertSuccess(epidb.add_biosource("HepG2", "hepatocellular carcinoma", {}, self.admin_key))
res, biosources = epidb.list_biosources(None, self.admin_key)
self.assertSuccess(res, biosources)
biosources_names = epidb.extract_names(biosources)[1]
self.assertEqual(len(biosources), 3)
self.assertTrue("K562" in biosources_names)
self.assertTrue("K562b" in biosources_names)
self.assertTrue("HepG2" in biosources_names)
status, _id = epidb.name_to_id(["k562", "k562b", "hepg2"], "biosources", self.admin_key)
self.assertTrue(_id, [['bs1', 'k562'], ['bs2', 'k562b'], ['bs3', 'hepg2']])
